Metadata-Version: 2.1
Name: dnachisel
Version: 3.2.6
Summary: Optimize DNA sequences under constraints.
Home-page: https://github.com/Edinburgh-Genome-Foundry/DnaChisel
Author: Zulko
License: MIT
Description: DNA Chisel
        ==========
        
        DNA Chisel (complete documentation `here <https://edinburgh-genome-foundry.github.io/DnaChisel/>`_)
        is a Python library for optimizing DNA sequences with respect to a set of
        constraints and optimization objectives. It comes with over 15 classes of
        sequence specifications which can be composed to, for instance, codon-optimize
        genes, meet the  constraints of a commercial DNA provider, avoid homologies
        between sequences, tune GC content, or all of this at once!
        
        DNA Chisel also allows users to define their own specifications in Python,
        making the library suitable for a large range of automated sequence design
        applications, and complex custom design projects. It can be used as a Python
        library, a command-line interface, or a `web application <https://cuba.genomefoundry.org/sculpt_a_sequence>`_.
        
        
        Example of use
        ---------------
        
        .. code:: python
        
            from dnachisel import *
        
            # DEFINE THE OPTIMIZATION PROBLEM
        
            some_sequence = random_dna_sequence(10000)
            problem = DnaOptimizationProblem(
                sequence=some_sequence,
                constraints=[
                    AvoidPattern("BsaI_site"),
                    EnforceGCContent(mini=0.3, maxi=0.7, window=50),
                    EnforceTranslation(location=(500, 1400))
                ],
                objectives=[CodonOptimize(species='e_coli', location=(500, 1400))]
            )
        
            # SOLVE THE CONSTRAINTS, OPTIMIZE WITH RESPECT TO THE OBJECTIVE
        
            problem.resolve_constraints()
            problem.optimize()
        
            # PRINT SUMMARIES TO CHECK THAT CONSTRAINTS PASS
        
            print(problem.constraints_text_summary())
            print(problem.objectives_text_summary())
        
        Alternatively, DNA Chisel lets you define problems by annotating a Genbank file.
        You can also define a problem by annotating directly a Genbank as follows:
        
        .. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/DnaChisel/master/docs/_static/images/example_sequence.png
           :alt: [logo]
           :align: center
           :width: 450px
        
        See `this page <https://edinburgh-genome-foundry.github.io/DnaChisel/ref/builtin_specifications.html>`_
        for an overview of available specifications.
        
        Infos
        -----
        
        **PIP installation:**
        
        .. code:: bash
        
          pip install dnachisel[reports]
        
        (you can omit the ``[reports]`` suffix if you intend to use dnachisel only
        for sequence optimization, without generating figures or PDF reports)
        
        **Web documentation:**
        
        `<https://edinburgh-genome-foundry.github.io/DnaChisel/>`_
        
        **Github Page**
        
        `<https://github.com/Edinburgh-Genome-Foundry/DnaChisel>`_
        
        **Live demo**
        
        `<http://cuba.genomefoundry.org/sculpt_a_sequence>`_
        
        **License:** MIT, Copyright Edinburgh Genome Foundry
        
        More biology software
        -----------------------
        
        .. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png
          :target: https://edinburgh-genome-foundry.github.io/
        
        DNA Chisel is part of the `EGF Codons <https://edinburgh-genome-foundry.github.io/>`_ synthetic biology software suite for DNA design, manufacturing and validation.
        
Keywords: DNA gene design codon optimization constraints synthetic biology
Platform: UNKNOWN
Provides-Extra: reports
